ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

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Electronic Resource

Neutral and Nonneutral Mitochondrial Genetic Variation in Deep-Sea Clams from the Family Vesicomyidae (2000)

Peek, Andrew S. ; Gaut, Brandon S. ; Feldman, Robert A. ; [et al.]

Springer

Journal of molecular evolution 50 (2000), S. 141-153

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ISSN: 1432-1432

Keywords: Key words: Nearly neutral variation — Synonymous — Nonsynonymous — Ribosomal RNA — Neutrality tests — Deep-sea chemoautotrophic bivalves

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract. Nucleotide sequences at two mitochondrial genes from 57 individuals representing eight species of deep-sea clams (Vesicomyidae) were examined for variation consistent with the neutral model of molecular evolution. One gene, cytochrome oxidase subunit I (COI), deviated from the expectations of neutrality by containing an excess of intraspecific nonsynonymous polymorphism. Additionally, one species, Calyptogena kilmeri, showed a significant excess of rare polymorphism specifically at the COI locus. In contrast, a second mitochondrial gene, the large-subunit 16S ribosomal RNA gene (16S), showed little deviation from neutrality either between or within species. Together, COI and 16S show no deviation from neutral expectations by the HKA test, produce congruent phylogenetic relationships between species, and show correlated numbers of fixed differences between species and polymorphism within species. These patterns of both neutral and nonneutral evolution within the mitochondrial genome are most consistent with a model where intraspecific nonsynonymous polymorphism at COI is near neutrality. In addition to examining the forces of molecular evolution, we extend hypotheses about interspecific relationships within this family for geographical locations previously unexamined by molecular methods including habitats near the Middle Atlantic, the Aleutian Trench, and Costa Rica.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002399910016

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2

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Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants (1992)

Gaut, Brandon S. ; Muse, Spencer V. ; Clark, W. Dennis ; [et al.]

Springer

Journal of molecular evolution 35 (1992), S. 292-303

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ISSN: 1432-1432

Keywords: rbcL ; Relative rates of nucleotide substitution ; Generation time ; Phylogeny construction

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Summary We subjected 35 rbcL nucleotide sequences from monocotyledonous taxa to maximum likelihood relative rate tests and estimated relative differences in rates of nucleotide substitution between groups of sequences without relying on knowledge of divergence times between taxa. Rate tests revealed that there is a hierarchy of substitution rate at the rbcL locus within the monocots. Among the taxa analyzed the grasses have the most rapid substitution rate; they are followed in rate by the Orchidales, the Liliales, the Bromeliales, and the Arecales. The overall substitution rate for the rbcL locus of grasses is over 5 times the substitution rate in the rbcL of the palms. The substitution rate at the third codon positions in the rbcL of the grasses is over 8 times the third position rate in the palms. The pattern of rate variation is consistent with the generation-time-effect hypothesis. Heterogenous rates of substitution have important implications for phylogenetic reconstruction.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00161167

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3

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Evolution in the Genus Zea: Lessons from Studies of Nucleotide Polymorphism (1996)

GAUT, BRANDON S.

Oxford, UK : Blackwell Publishing Ltd

Plant species biology 11 (1996), S. 0

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ISSN: 1442-1984

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Abstract The genus Zea consists of the cultivar maize and six wild taxa. All taxa in the genus hybridize with one another, and the genus appears to be of relatively recent origin. The genus Zea has long been of interest to evolutionary and molecular geneticists, and a plethora of studies have established that maize and the teosintes are genetically diverse. This high diversity, coupled with relatively recent divergence among taxa, makes Zea an excellent model system for studying the distribution of nucleotide diversity both among recently diverged taxa and among a crop and its wild relatives. Nucleotide diversity has been studied in a number of maize loci. These studies have documented tremendous nucleotide variation in maize, and they suggest that allelic lineages in the maize gene pool can be quite long-lived. For example, it has been estimated that allelic lineages have existed for several million years at both the Adh 1 and the Adh2 locus, suggesting that the common ancestor to Zea taxa was highly polymorphic. These studies have also found ample evidence of recombination in maize loci, suggesting that recombination plays an important role in generating haplotype diversity. A recent study of the regulatory locus c1, a regulatory gene in the anthocyanin biosynthesis pathway, belies this general picture. Alleles from the c1 locus have been sampled from maize and teosintes. The sampled alleles fall into two discrete groups, corresponding to two distinct functional classes. Both classes are found in teosinte, but only one of these classes is found in maize. The c1 locus is less diverse than any other maize locus yet examined. It is hypothesized that low nucleotide diversity at the c1 locus is a consequence of selection, probably artificial by the early domesticators of maize.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1442-1984.1996.tb00103.x

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4

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A unified mixed-model method for association mapping that accounts for multiple levels of relatedness (2006)

Yu, Jianming ; Pressoir, Gael ; Briggs, William H ; [et al.]

[s.l.] : Nature Publishing Group

Nature genetics 38 (2006), S. 203-208

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ISSN: 1546-1718

Source: Nature Archives 1869 - 2009

Topics: Biology , Medicine

Notes: [Auszug] As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by ...

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1038/ng1702

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5

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The paleontology of intergene retrotransposons of maize (1998)

SanMiguel, Phillip ; Gaut, Brandon S. ; Tikhonov, Alexander ; [et al.]

[s.l.] : Nature America Inc.

Nature genetics 20 (1998), S. 43-45

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ISSN: 1546-1718

Source: Nature Archives 1869 - 2009

Topics: Biology , Medicine

Notes: [Auszug] Retrotransposons, transposable elements related to animal retroviruses, are found in all eukaryotes investigated and make up the majority of many plant genomes. Their ubiquity points to their importance, especially in their contribution to the large-scale structure of complex genomes. The ...

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1038/1695

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6

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Assessing the Abundance and Polymorphism of Simple Sequence Repeats in Perennial Ryegrass (1999)

Kubik, Christine ; Meyer, William A. ; Gaut, Brandon S.

Springer

Crop science 39 (1999), S. 1136-1141

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ISSN: 1435-0653

Source: Springer Online Journal Archives 1860-2000

Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Lolium perenne L.). A library of perennial ryegrass genomic DNA was screened with (GA) n and (GT) n probes, and SSR-containing clones were isolated and sequenced. On the basis of this screen, we estimated that there are roughly 5800 (GA) n and (GT) n SSRs in the haploid perennial ryegrass genome. Polymerase chain reaction (PCR) primers were designed to amplify the isolated SSRs, and six polymorphic SSRs were identified. Polymorphism in these six SSRs was sufficient to discriminate among 18 individuals represent 11 perennial ryegrass clones and seven other Lolium species. Half-sibs could be distinguished with data from as few as three SSRs. The SSR genotype data was also use to infer genetic relationships among the individuals of our sample. The relationships were in broad agreement with those established by previous analyses, suggesting that SSR data will be useful for exploring relationships among perennial ryegrass cultivars. In total, this study indicates that SSRs are sufficiently abundant and sufficiently polymorphic to be useful genetic markers in perennial ryegrass.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/

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7

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Evolution of genes and taxa: a primer (2000)

Doyle, Jeff J. ; Gaut, Brandon S.

Springer

Plant molecular biology 42 (2000), S. 1-23

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ISSN: 1573-5028

Keywords: homology ; molecular population genetics ; multigene families ; phylogenetic methods ; rates of molecular evolution

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for example, is a central theme in evolutionary biology whose definition is complex and often controversial. Homology extends to multigene families, where the distinction between orthology and paralogy is key. Nucleotide sequence alignment is also a homology issue, and is a key stage in any evolutionary analysis of sequence data. Models based on our understanding of the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes between aligned sequences and in phylogeny reconstruction from sequence data. The three common methods of phylogeny reconstruction – parsimony, distance and maximum likelihood – differ in their use of these models. All three face similar problems in finding optimal – and reliable – solutions among the vast number of possible trees. Moreover, even optimal trees for a given gene may not reflect the relationships of the organisms from which the gene was sampled. Knowledge of how genes evolve and at what rate is critical for understanding gene function across species or within gene families. The Neutral Theory of Molecular Evolution serves as the null model of molecular evolution and plays a central role in data analysis. Three areas in which the Neutral Theory plays a vital role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of molecular clocks, and providing a foundation for molecular population genetics.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1006349518932

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Evolutionary genomics of grape (Vitis viniferassp.vinifera) domestication (2017)

Zhou, Yongfeng ; Massonnet, Mélanie ; Sanjak, Jaleal S. ; [et al.]

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences of the United States of America. 2017; 114(44): 11715-11720. Published 2017 Oct 17. doi: 10.1073/pnas.1709257114.

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Publication Date: 2017-10-17

Description: We gathered genomic data from grapes (Vitis viniferassp.vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General